For rest of your post, I would need more than "factory/warehouse", it seems you are (in my opinion) doing it a bit backwards, you want to design a place the runners have to break in to, and THEN figure out why. I think the best results are the other way around. Why do they need to go there?, then figure out what a reasonable defense layout for the facility is.
I like to make security layouts in case my players jump me with some surprising turn of events. I had to build a semi-secure construction site on the fly once because my players wanted a dump truck and didn't want to pay.
Basically, I'm trying to build a medium level storage facility and change some variables based on whatever my runners want to get from it. Rare prototype thingamajig? More guards, drones, and better node security. The left shoe off a middle manager? Force 5 fire elemental 
The answer to your question is:
Whatever the hell you want.
A) Response times can vary wildly based on Crime levels, How busy the Cops are in the area, and anything up to Bribes the watch commander is taking that week... it's entirely up to you.
B) Magical support depends on what the Corp/Organisation feels like paying.
- You want Shamans with trained Barghests on every door and a Bound Force 10 elemental over the shoulder of each guard? Done.
- You want nothing more than a watcher spirit patrolling every hour or so. Done
- You want FAB and a Feathered Serpent waiting in the warehouse? Done.
- It's your show... and the only query is whether the corp thinks the target is worth that much protection...
C) Physical Stats for the towers can be whatever you want. I'd recommend just basing them in sections (maybe 4 high) with a particular structure rating of your choice. Taking down a bottom section may weaken higher ones...that sort of thing)...
D) TacNets can do cool things. For simplicity's sake though, I'd recommend just adding a few dice to each guard, and giving every one of them full access to what any of them notice. (TacNets are great, but using them for every guard at the facility may slow you down. The PC's are the stars of the show, not the security goons...)
Like 'Man who walks at night' I think you're doing this backwards.... IMHO.